Re: [AMBER] Nastruct reference file format

From: Daniel Roe <>
Date: Fri, 4 Jun 2021 13:30:57 -0400

Hi, sorry for the delay in replying here.

On Fri, Jun 4, 2021 at 11:42 AM Robert Molt <> wrote:
> 1.) "Underlying" meaning the custom nucleic acid is "most like" one of
> the traditional nucleic acids? If so, what defines this property? In my
> case, I have custom nucleic acids which are pretty different from the
> natural nucleic acids. In fact, in one case, I have an amino acid which
> has inserted into a DNA helix to replace a nucleic acid (poorly).

So cpptraj will calculate any hydrogen bonds between nucleic acid
bases using the atoms designated as donor or acceptor. However, it
categorizes hydrogen bonds between G-C or A-T/U bases as Watson-Crick
(WC); if the base is a name not recognized as G, C, A, T, or U it just
won't consider any of the hydrogen bonds as WC hydrogen bonds.

> 2.) What do "G G G5 G3" signify, in the example of guanine? What do each
> of the letters/numbers indicate?

So as stated in the manual regarding this line:

<base character> <res name 0> [<res name 1> ...]

So the first character is the "base character". It can be anything,
but A, C, G, T, and U have significance for determining whether
hydrogen bonds are WC (as mentioned above). The remaining entries are
residue names that map to this reference base, in this case G, G5 (5'
terminal G) and G3 (3' terminal G). Does that make sense? Let me know
if not.


> --
> Dr. Robert Molt Jr.
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Received on Fri Jun 04 2021 - 11:00:02 PDT
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